GENE SET ENRICHMENT ANALYSIS MADE SIMPLE

Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to quantify the interest of each gene with a p-value, adjust these p-values for multiple comparisons, chose an appropriate cut-off, and create a list of candidate genes. This approach has been criticized for ignoring biological knowledge regarding how genes work together. Recently a series of methods, that do incorporate biological knowledge, have been proposed. However, many of these methods seem overly complicated. Furthermore, the most popular method, Gene Set Enrichment Analysis (GSEA), is based on a statistical test known for its lack of sensitivity. In this paper we compare the performance of a simple alternative to GSEA.We find that this simple solution clearly outperforms GSEA.We demonstrate this with eight different microarray datasets.

Analysis of atmospheric transport and the effects of seasonal and interannual transport variability on measurements made at the Pico Mountain observatory

A non-hierarchical K-means algorithm is used to cluster 47 years (1960–2006) of 10-day HYSPLIT backward trajectories to the Pico Mountain (PM) observatory on a seasonal basis. The resulting cluster centers identify the major transport pathways and collectively comprise a long-term climatology of transport to the observatory. The transport climatology improves our ability to interpret the observations made there and our understanding of pollution source regions to the station and the central North Atlantic region. I determine which pathways dominate transport to the observatory and examine the impacts of these transport patterns on the O3, NOy, NOx, and CO measurements made there during 2001–2006. Transport from the U.S., Canada, and the Atlantic most frequently reaches the station, but Europe, east Africa, and the Pacific can also contribute significantly depending on the season. Transport from Canada was correlated with the North Atlantic Oscillation (NAO) in spring and winter, and transport from the Pacific was uncorrelated with the NAO. The highest CO and O3 are observed during spring. Summer is also characterized by high CO and O3 and the highest NOy and NOx of any season. Previous studies at the station attributed the summer time high CO and O3 to transport of boreal wildfire emissions (for 2002–2004), and boreal fires continued to affect the station during 2005 and 2006. The particle dispersion model FLEXPART was used to calculate anthropogenic and biomass-burning CO tracer values at the station in an attempt to identify the regions responsible for the high CO and O3 observations during spring and biomass-burning impacts in summer.

Processing and characterization of PbSnTe-based thermoelectric materials made by mechanical alloying

The research reported in this dissertation investigates the processes required to mechanically alloy Pb1-xSnxTe and AgSbTe2 and a method of combining these two end compounds to result in (y)(AgSbTe2)–(1 - y)(Pb1-xSnxTe) thermoelectric materials for power generation applications. In general, traditional melt processing of these alloys has employed high purity materials that are subjected to time and energy intensive processes that result in highly functional material that is not easily reproducible. This research reports the development of mechanical alloying processes using commercially available 99.9% pure elemental powders in order to provide a basis for the economical production of highly functional thermoelectric materials. Though there have been reports of high and low ZT materials fabricated by both melt alloying and mechanical alloying, the processing-structure-properties-performance relationship connecting how the material is made to its resulting functionality is poorly understood. This is particularly true for mechanically alloyed material, motivating an effort to investigate bulk material within the (y)(AgSbTe2)–(1 - y)(Pb1-xSnx- Te) system using the mechanical alloying method. This research adds to the body of knowledge concerning the way in which mechanical alloying can be used to efficiently produce high ZT thermoelectric materials. The processes required to mechanically alloy elemental powders to form Pb1-xSnxTe and AgSbTe2 and to subsequently consolidate the alloyed powder is described. The composition, phases present in the alloy, volume percent, size and spacing of the phases are reported. The room temperature electronic transport properties of electrical conductivity, carrier concentration and carrier mobility are reported for each alloy and the effect of the presence of any secondary phase on the electronic transport properties is described. An mechanical mixing approach for incorporating the end compounds to result in (y)(AgSbTe2)–(1-y)(Pb1-xSnxTe) is described and when 5 vol.% AgSbTe2 was incorporated was found to form a solid solution with the Pb1-xSnxTe phase. An initial attempt to change the carrier concentration of the Pb1-xSnxTe phase was made by adding excess Te and found that the carrier density of the alloys in this work are not sensitive to excess Te. It has been demonstrated using the processing techniques reported in this research that this material system, when appropriately doped, has the potential to perform as highly functional thermoelectric material.

HAMLET (human alpha-lactalbumin made lethal to tumor cells) triggers autophagic tumor cell death

HAMLET, a complex of partially unfolded alpha-lactalbumin and oleic acid, kills a wide range of tumor cells. Here we propose that HAMLET causes macroautophagy in tumor cells and that this contributes to their death. Cell death was accompanied by mitochondrial damage and a reduction in the level of active mTOR and HAMLET triggered extensive cytoplasmic vacuolization and the formation of double-membrane-enclosed vesicles typical of macroautophagy. In addition, HAMLET caused a change from uniform (LC3-I) to granular (LC3-II) staining in LC3-GFP-transfected cells reflecting LC3 translocation during macroautophagy, and this was blocked by the macroautophagy inhibitor 3-methyladenine. HAMLET also caused accumulation of LC3-II detected by Western blot when lysosomal degradation was inhibited suggesting that HAMLET caused an increase in autophagic flux. To determine if macroautophagy contributed to cell death, we used RNA interference against Beclin-1 and Atg5. Suppression of Beclin-1 and Atg5 improved the survival of HAMLET-treated tumor cells and inhibited the increase in granular LC3-GFP staining. The results show that HAMLET triggers macroautophagy in tumor cells and suggest that macroautophagy contributes to HAMLET-induced tumor cell death.

Semi-Automated Creation of Converged iTV Services: From Macromedia Director Simulations to Services Ready for Broadcast

While sound and video may capture viewers' attention, interaction can captivate them. This has not been available prior to the advent of Digital Television. In fact, what lies at the heart of the Digital Television revolution is this new type of interactive content, offered in the form of interactive Television (iTV) services. On top of that, the new world of converged networks has created a demand for a new type of converged services on a range of mobile terminals (Tablet PCs, PDAs and mobile phones). This paper aims at presenting a new approach to service creation that allows for the semi-automatic translation of simulations and rapid prototypes created in the accessible desktop multimedia authoring package Macromedia Director into services ready for broadcast. This is achieved by a series of tools that de-skill and speed-up the process of creating digital TV user interfaces (UI) and applications for mobile terminals. The benefits of rapid prototyping are essential for the production of these new types of services, and are therefore discussed in the first section of this paper. In the following sections, an overview of the operation of content, service, creation and management sub-systems is presented, which illustrates why these tools compose an important and integral part of a system responsible of creating, delivering and managing converged broadcast and telecommunications services. The next section examines a number of metadata languages candidates for describing the iTV services user interface and the schema language adopted in this project. A detailed description of the operation of the two tools is provided to offer an insight of how they can be used to de-skill and speed-up the process of creating digital TV user interfaces and applications for mobile terminals. Finally, representative broadcast oriented and telecommunication oriented converged service components are also introduced, demonstrating how these tools have been used to generate different types of services.

Italia: La chiusura della Casa dell’Emigrante come spunto riflessione sui rientri degli emigrati italiani

In the literature on migration, as well as in social policies regarding this phenomenon, the situation of returning emigrants receives scant attention. This essay establishes an intricate connection between attitudes and policies that prevail in a country regarding emigration and those concerning immigration. The case of Italy provides a prime example for this as it once was a classical country of emigration, only to turn, in recent decades, into a country that appears highly attractive (and relatively accessible) to immigrants. The essay traces the pervasive ambiguity that characterizes this country’s attitudes towards emigration from the beginning of mass emigration shortly after the unification of Italy in 1868 to the emigration policies of the fascist regime of Mussolini and the post-World War II waves of emigration right through to the corresponding ambiguity concerning the status of immigrants in contemporary society, including the indifferent treatment of returning Italian emigrants who constitute a considerable numerical phenomenon. These reflections take their origin from the impending closure of a reception centre in Lazio, the Casa dell’Emigrante near Sant’Elia Fiumerapido, Province of Frosinone, ostensibly for financial reasons. This centre had been the only one of its kind in the whole of Italy dealing officially with the needs of repatriated Italians. It had assisted returning emigrants both with practical matters, such as negotiating the labyrinth of Italian bureaucracy , and with psychological implications of a return, which are often considerable given the time lag of experiences with current social realities and the frequently unrealistic expectations associated with the return. Questions of identity become highly acute in those circumstances. The threatened closure of the centre illustrates the unwillingness of the state to face up to the factual prevalence of migratory experiences in the country as a whole and as a core element of national history, experiences of migration in both directions. The statistics speak for themselves: of the 4.660.427 persons who left Italy between 1880 and 1950, 2.322.451 have returned, almost exactly 50%. To those have to be added 3.628.430 returnees of the 5.109.860 emigrants who left Italy between the end of World War II and 1976 for Europe alone. Attitudes towards people leaving changed ostensibly over time. In the first two decades after Unification parliament on the one hand wanted to show some concern over the fate of its citizens, not wanting to abandon those newly created citizens entirely to their own destiny, while on the other portraying their decisions to emigrate as expressions of individual liberty and responsibility and not necessitated by want and poverty. Emigrants had to prove, paradoxically that they had the requisite means to emigrate when in fact poverty was largely driving them to emigrate. To admit that publicly would have amounted to admission of economic and political failure made evident through emigration. In contrast to that Mussolini’s emigration policies not only enforced large population movements within the territory of Italy to balance unemployment between regions and particularly between North and South, but also declared it citizen’s duty to be ready to move also to the colonies, thereby ‘turning emigration as a sign of social crisis into a sign of national strength and the success of the country’s political agenda’ (Gaspari 2001, p. 34). The duplicity continued even after World War II when secret deals were done with the USA to allow a continuous flow of Italian immigrants and EU membership obviously further facilitated the departure of unemployed, impoverished Italians. With the growing prosperity of Italy the reversal of the direction of migration became more obvious. On the basis of empirical research conducted by one of the author on returning emigrants four types of motives for returning can be distinguished: 1. Return as a result of failure – particularly the emigrants who left during the 1950-1970 period usually had no linguistic preparation, and in any case the gap between the spoken and the written language is enormous with the latter often being insurmountable. This gives rise to nostalgic sentiments which motivates a return into an environment where language is familiar 2. Return as a means of preserving an identity – the life of emigrants often takes place within ghetto-like conditions where familiarity is being reproduced but under restricted conditions and hence not entirely authentic. The necessity for saving money permits only a partial entry into the host society and at the same time any accumulating savings add to the desire to return home where life can be lived fully again – or so it seems. 3. Return of investment – the impossibility to become fully part of another society often motivates migrants to accumulate not so much material wealth but new experiences and competences which they then aim to reinvest in their home country. 4. Return to retire – for many emigrants returning home becomes acute once they leave a productive occupation and feelings of estrangement build up, in conjunction with the efforts of having invested in building a house back home. All those motives are associated with a variety of difficulties on the actual return home because, above all, time in relation to the country of origin has been suspended for the emigrant and the encounter with the reality of that country reveals constant discrepancies and requires constant readjustment. This is where the need for assistance to returning emigrants arises. The fact that such an important centre of assistance has been closed is further confirmation of the still prevailing politics of ambiguity which nominally demand integration from nationals and non-nationals alike but deny the means of achieving this. Citizenship is not a natural result of nationality but requires the means for active participation in society. Furthermore, the experiences of returning immigrants provide important cues for the double ambivalence in which immigrants to Italy live between the demands made on them to integrate, the simultaneous threats of repatriation and the alienation from the immigrants’ home country which grows inexorably during the absence. The state can only regain its credibility by putting an end to this ambiguity and provide to returning emigrants, and immigrants alike, the means of reconstructing strong communal identities.

Virtual characters designed for forensic assessment and rehabilitation of sex offenders: standardized and made-to-measure

This paper presents two studies pertaining to the use of virtual characters applied in clinical forensic rehabilitation of sex offenders. The first study is about the validation of the perceived age of virtual characters designed to simulate primary and secondary sexual character of typical adult and child individuals. The second study puts to use these virtual characters in comparing a group of sex offenders and a group of non deviant individuals on their sexual arousal responses as recorded in virtual immersion. Finally, two clinical vignettes illustrating the use of made-to-measure virtual characters to more closely fit sexual preferences are presented in Discussion.